NM_001099658.2:c.13C>A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001099658.2(LRRN3):c.13C>A(p.Pro5Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,611,726 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099658.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRN3 | ENST00000308478.10 | c.13C>A | p.Pro5Thr | missense_variant | Exon 3 of 3 | 1 | NM_001099658.2 | ENSP00000312001.5 | ||
IMMP2L | ENST00000405709.7 | c.240-159220G>T | intron_variant | Intron 3 of 5 | 1 | NM_032549.4 | ENSP00000384966.2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248684Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134242
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459562Hom.: 1 Cov.: 33 AF XY: 0.00000827 AC XY: 6AN XY: 725926
GnomAD4 genome AF: 0.000105 AC: 16AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13C>A (p.P5T) alteration is located in exon 4 (coding exon 1) of the LRRN3 gene. This alteration results from a C to A substitution at nucleotide position 13, causing the proline (P) at amino acid position 5 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at